[BioC] XYS from nimblegen

[Benilton Carvalho]

Marcelo,

do you have access to the NimbleScan software? It is as simple as
selecting Report / XYS (or something similar to that) e pointing to
the TIFF images for which you want the XYS files.

For PAIR -> XYS, please check the following thread:

http://comments.gmane.org/gmane.science.biology.informatics.conductor/27547

If you still find problems, please contact me off-list... and I'll get
back to the list once things work out.

b

2010/7/12 Marcelo Brandão <brandao.marcelo at gmail.com>:
> Hello there.
> Does anyone knows how to generate XYS file from nimblegen pair file?
> I am having a lot of problem trying to do accomplish this and analyze
> my data thru bioconductor.
> I have two main errors.
> One if I try to read xys file a receive this:
>> dat <- read.xysfiles(xys_files)
> Platform design info loaded.
> Checking designs for each XYS file... Done.
> Allocating memory... Error in smartReadXYS(filenames, sampleNames) :
>  negative extents to matrix
> OR
> When i am building annotation package:
>
>> makePdInfoPackage(seed, destDir = ".")
> ================================================================================
> Building annotation package for Nimblegen Expression Array
> NDF: 2006-08-18_TI4932_60mer.ndf
> XYS: 50186202_532.xys
> ================================================================================
> Parsing file: 2006-08-18_TI4932_60mer.ndf... OK
> Parsing file: 50186202_532.xys... OK
> Merging NDF and XYS files... OK
> Preparing contents for featureSet table... OK
> Preparing contents for bgfeature table... OK
> Preparing contents for pmfeature table... OK
> Error in parseNgsPair(object at ndfFile, object at xysFile, verbose = !quiet) :
>  Control probe possibly identified as Experimental
>
>
> I know, I Know, this seems to be easy, but I can not understand what
> is going on!!!
>
> Thanks in advance for all of list members for your time reading this.
>
> My best regards
>
> Marcelo
>
>
> --
> Marcelo Mendes Brandão
> Postdoc fellow
> Laboratório de Biologia Molecular de Plantas - ESALQ/USP
> Website: http://bioinfo.esalq.usp.br
> AtPIN: http://bioinfo.esalq.usp.br/atpin
> SKYPE: mmbrand
> Tel: (+55) 19 3429 4442
>
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